# XFMS workflow simple

**T2-to-T1 registration**
*Step 1: Register cropped T2 to cropped T1*
out: T2w_registered_to_T1w.nii.gz and cropT2tocropT1.mat

**Apply identity matrix to T1 and T2 to resize**
*Step 1: Apply identity matrix to cropped T1*
out: T1w_to_BIBS.nii.gz and crop_T1w_to_BIBS_template.mat

*Step 2: Apply identity matrix to T1-registered cropped T2*
out: T2w_to_BIBS.nii.gz and crop_T2w_to_BIBS_template.mat

**Concatenate matrices and apply to average T1/T2 to result in output files with correct size and resolution**
*Step 1: T1w - concatenate full2cropT1w.mat and crop_T1w_to_BIBS_template.mat to make full_crop_T1w_to_BIBS_template.mat*

*Step 2: T1w- apply full_crop_T1w_to_BIBS_template.mat to average T1 to make preBIBSnet_final_0000.nii.gz*

*Step 3: T2w - concatenate full2cropT2w.mat and cropT2tocropT1.mat to create intermediate full2cropT2toT1.mat that captures cropping and T2-T1 registration*

*Step 4: T2w - concatenate intermediate full2cropT2toT1.mat and crop_T2w_to_BIBS_template.mat to make full_crop_T2w_to_BIBS_template.mat*

*Step 5: T2w - apply full_crop_T2w_to_BIBS_template.mat to average T2 to get preBIBSnet_final_0001.nii.gz*